AMINO ACIDS AND PROTEINS (LECTURE 1) Flashcards
(protein) monomers are called…
amino acids.
(protein) polymers are called… (2)
polypeptides or proteins.
amino acids are linked by…
peptide bonds.
What is the difference between a protein and a polypeptide? (2)
Proteins can be up of 1 or more polypeptides and they serve a function (unlike polypeptides).
List a few protein functions. (5)
Enzymes, protein hormones (insulin), transport, cell movement, structural.
Amino acids are made up of 4 components that are all attached to what?
A central carbon.
What are the 4 components connected by a central carbon in an amino acid?
A hydrogen, a carboxyl group, an amino group and a R group (side chain).
How many different amino acids are there?
20
Is the amino group the acidic or basic component of an amino acid?
The amino group is the basic component.
Is the carboxyl group the acidic or basic component of an amino acid?
The carboxyl group is the acidic component.
What is the significance of the R group (side chain)?
The R group is the only varying component for each of the 20 different amino acids and thus determines the characteristics of an amino acid.
What components make up the backbone of an amino acid?
The central carbon, the hydrogen, the carboxyl group and the amino group.
How are amino acids classified? (2)
As either hydrophobic or hydrophilic.
Hydrophobic amino acids have…
non polar side chains.
Hydrophilic amino acids have… (2)
polar (but uncharged) side chains or charged side chains.
When is a charged amino acid considered acidic? Is it positively or negatively charged (at pH 7)?
When the side chain contains a carboxylic acid (COOH / COO-). It is negatively charged at pH 7 (COO-).
When is a charged amino acid considered basic? Is it positively or negatively charged (at pH 7)?
When the side chain contains a amino group (NH2 / NH3+). It is positively charged at pH 7 (NH3+).
The R group of a hydrophobic/non-polar amino acid is usually made up of what? (2)
They’re made up of only carbons and hydrogens.
What 2 non-polar amino acids are not made up from only carbon and hydrogen?
Methionine (contains S) and tryptophan (contains N).
The R group of a hydrophilic/polar amino usually contains what? What does it certainly lack? (2)
They contain oxygen atoms and lack COOH/COO- (carboxylic acids).
Which polar amino acid does not have an oxygen atom? What makes it polar instead?
Cysteine is polar because its side chain contains an SH molecule, rather than an oxygen atom.
How can you tell whether the amino acid shown is being shown at pH 7?
If the backbone’s amino group is positively charged and the backbone’s carboxyl group is negatively charged, then the amino acid shown is at pH 7.
What chemical formulas can be used to describe an amino acid’s carboxyl and amino groups at pH < 2?
NH3+ and COOH
What chemical formulas can be used to describe an amino acid’s backbone’s carboxyl and amino groups at pH = 7?
NH3+ and COO-
What chemical formulas can be used to describe an amino acid’s backbone’s carboxyl and amino groups at pH > 10?
NH2 and COO-
What characterizes the 3 ionic states in which amino acids can exist?
At pH < 2, at pH = 7 and at pH > 10.
On what does the overall charge of a protein depend? (2)
The sum of the charges of the amino acids is the overall charge of the protein. pH also determines the overall charge.
What is the pI of a protein?
The isoelectric point (pI) of a protein is the pH at which that protein has a neutral charge.
When pH = pI, what is the charge of the protein?
neutral
When pH > pI, what is the charge of the protein?
negative
When pH < pI, what is the charge of the protein?
positive
Amino acids are linked by ____ which are formed by ____ reactions.
Amino acids are linked by peptide bonds which are formed by dehydration reactions.
Polypeptides have directionality, meaning what?
Meaning they have two distinct ends.
What names do we give to the ends of a polypeptide?
The N-terminus (the amino group) and the C-terminus (the carboxyl group).
Why can proteins carry out so many diverse functions in cells?
Because there are 20 different amino acids, meaning there are many different possible combinations to make up a protein which means that protein can carry out many different functions.
What are the 4 levels of protein structure?
Primary structure, secondary structure, tertiary structure and quaternary structure.
Describe the primary structure of a protein. (4)
It is the linear sequence of amino acids coded for by a gene sequence (and linked by peptide bonds). It is thus determined by the DNA sequence and it has directionality (N terminus to C terminus).
Describe the secondary structure of a protein. (3)
It is the spatial arrangement of amino acids to form alpha helices or beta sheets. These are formed by the H-bonding between amino (N-H) and carboxyl (C=O) groups of the polypeptide backbone. The R-groups are not involved at this point.
Describe the a-helix (alpha helix). (3)
There are about 3.6 amino acids per turn. H-bonding occurs between amino acids spaced 4 places apart (aa1-aa5, aa2-aa6, etc.). Side chains are oriented away from the axis (center) of the a-helix.
Describe b-sheets (beta sheets). (2)
2 regions of the polypeptide chain lie parallel to each other (like a folded sheet). Arrows are used to show a b-sheet’s directionality (n to c terminus).
Can the same polypeptide form both a-helices and b-sheets?
Yes, it isn’t necessarily one or the other.
Do R groups participate in secondary structure bonding? Do they have any impact on the secondary structure at all?
No, R groups do not participate in the H-bonding that occurs during the formation of the secondary structure. However, R groups do have an influence on whether a polypeptide will take the shape of an a-helix or/and b-sheets.
Describe the tertiary structure of a protein. (3)
a-helices and b-sheets interact to form a variety of shapes. These shapes are formed through the interactions between amino acid side chains (R groups). Many tertiary structures are possible.
In the formation of a protein’s tertiary structure, what types of interactions occur between the side chains? Which of these is stronger than the other? (2)
Side chains interact through covalent (strong) and non-covalent interactions to form the tertiary structure.
What are the non-covalent (weak) interactions that can occur during the formation of a protein’s tertiary structure? (4)
Hydrogen bonds (between polar amino acids). Hydrophobic interactions (between non-polar amino acids). Van der Waals. Ionic bonds - or - salt bridges (between charged amino acids).
What is the covalent (strong) interaction that can occur during the formation of a protein’s tertiary structure? What are some of it’s characteristics? (2 characterisitcs)
A disulphide bridge - or - disulphide bond can form, but only between two cysteine amino acids and oxidation is required to make this bond.
Describe the quaternary structure of a protein. (2)
The quaternary structure of a protein forms when more than one polypeptide chain interact together to form a protein. These polypeptides are held together by the same interactions used to form the tertiary structure.
If a protein is composed of 3 subunits, this means that the protein is made up of ____ ____.
If a protein is composed of 3 subunits, this means that the protein is made up of 3 polypeptides.
Describe the process of denaturation. (2)
The denaturation of a protein is the disruption of that proteins structure (unfolding). Only the primary structure is left.
Can a denatured protein be renatured? (2)
Yes, but it is often difficult to do so.
What conditions could denature proteins? (5)
Change in temperature, change in pH, presence of salt, presence of a detergent and presence of reducing agents can all denature a protein.
In what way does a change in temperature denature proteins?
A change in temperature alters the vibrational and rotational energy and disrupts non-covalent interactions such as H-bonds.
In what way does a change in pH denature proteins? What does it do to specific side chains?
A change in pH changes the ionic state (the charge) of charged side chains.
In what way does the presence of salt denature proteins?
Salt changes the ionic environment and thus affects ionic bonds within the protein.
In what way does the presence of detergents denature proteins? (3)
Detergents disrupt hydrophobic interactions. Hydrophobic side chains move from the interior to the exterior of a protein. Hydrophilic side chains move towards the interior of a protein.
In what way does the presence of reducing agents denature proteins? Which amino acid does this affect the most?
Reducing agents break the covalent disulfide bonds that can form between two cysteine amino acids.
Which protein structures are affected by the denaturation of a protein?
The secondary, tertiary and quaternary structures are affected by the denaturation of a protein.
